SMTL ID : 7w3e.1 (1 other biounit)

Bovine cytochrome c oxidese in CN-bound fully reduced state at 50 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-2-2-2-1-1-2-2-1-1-2-1-1-1-mer

Ligands

4 x HEA: HEME-A(Non-covalent)

HEA.1: 36 residues within 4Å: Chain A: A.24, G.27, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 Ligands: TGL.7 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:I.389, A:F.393, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 30 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, V.320, G.352, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: CYN.6 34 PLIP interactions: 29 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126 Water bridges: A:Y.244, A:H.291, A:T.316, A:D.369, A:D.369 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Stacking: A:H.290 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.58: 35 residues within 4Å: Chain N: A.24, G.27, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 37 PLIP interactions: 37 interactions with chain N, Hydrophobic interactions: N:A.24, N:T.31, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:F.377, N:F.377, N:L.381, N:L.381, N:I.389, N:F.393, N:F.393, N:T.424, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:R.38, N:Y.54, N:W.126, N:Y.371, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438, N:S.461 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.59: 30 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, V.320, G.352, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain O: I.34, P.69, I.72, L.73 Ligands: CYN.63 34 PLIP interactions: 29 interactions with chain N, 5 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:T.316, N:V.320, N:I.356, N:V.373, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, N:L.381, O:I.34, O:I.34, O:P.69, O:I.72, O:L.73 Hydrogen bonds: N:W.126 Water bridges: N:Y.244, N:T.316, N:D.369, N:D.369 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240, N:H.240 Metal complexes: N:H.376

2 x CU: COPPER (II) ION(Non-covalent)

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CYN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.60: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: CYN.63 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N:H.291

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.14, H2O.14, H2O.16 MG.61: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 6 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.84, H2O.84, H2O.85

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43 NA.27: 3 residues within 4Å: Chain C: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.234 NA.62: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:D.442 Water bridges: N:Q.43 NA.82: 3 residues within 4Å: Chain P: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:E.234

2 x CYN: CYANIDE ION(Non-covalent)

CYN.6: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) CYN.63: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.59, CU.60 No protein-ligand interaction detected (PLIP)

5 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.7: 27 residues within 4Å: Chain A: T.17, L.18, L.20, L.21, F.22, W.25, P.106, F.109, L.110, L.112, L.113, F.393, F.400, S.401, I.472 Chain L: N.9, I.10, P.11, F.12, S.13, R.19, M.23, M.24, F.27, F.28, S.30 Ligands: HEA.1 22 PLIP interactions: 6 interactions with chain L, 16 interactions with chain A Hydrophobic interactions: L:I.10, L:F.12, L:F.27, L:F.27, L:F.28, L:F.28, A:T.17, A:L.18, A:L.20, A:L.21, A:F.22, A:W.25, A:W.25, A:P.106, A:F.109, A:F.109, A:L.112, A:L.113, A:L.113, A:F.393, A:F.393, A:I.472 TGL.18: 17 residues within 4Å: Chain A: F.346, T.354, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 18 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.28, B:V.31, B:F.32, B:F.32, B:F.32, B:L.39, A:F.346, A:T.354, A:N.422, A:F.426, A:F.426, A:F.426, A:F.426, A:F.430, A:F.430 Water bridges: B:G.8 Salt bridges: B:H.24, I:R.43 TGL.37: 17 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.346, F.414, A.415, F.418 Chain B: L.39, I.42, S.43 Chain D: R.70, S.71, T.72, E.74, W.75, I.86 16 PLIP interactions: 6 interactions with chain D, 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:W.75, D:I.86, A:W.334, A:W.334, A:W.334, A:L.342, A:F.346, A:F.414, A:F.418, B:L.39, B:I.42 Hydrogen bonds: D:T.72, D:E.74, D:W.75 Water bridges: D:T.72 Salt bridges: A:K.411 TGL.73: 15 residues within 4Å: Chain N: T.354, Y.379, N.422, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, S.35, L.39 13 PLIP interactions: 7 interactions with chain N, 6 interactions with chain O Hydrophobic interactions: N:T.354, N:N.422, N:F.426, N:F.426, N:F.426, N:H.429, N:F.430, O:L.7, O:V.31, O:F.32, O:F.32 Water bridges: O:G.8 Salt bridges: O:H.24 TGL.74: 11 residues within 4Å: Chain N: W.334, L.342, F.346, K.411, F.414, A.415 Chain O: L.39, I.42, S.43, L.46, T.47 12 PLIP interactions: 8 interactions with chain N, 4 interactions with chain O Hydrophobic interactions: N:W.334, N:W.334, N:L.342, N:F.346, N:K.411, N:F.414, N:F.414, O:L.39, O:I.42, O:L.46, O:T.47 Salt bridges: N:K.411

7 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.8: 11 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16, S.20 16 PLIP interactions: 5 interactions with chain A, 2 interactions with chain M, 4 interactions with chain K, 5 interactions with chain D Hydrophobic interactions: A:T.408, A:W.409, A:W.409, M:P.12, M:Q.15, K:F.4, K:F.4, D:A.81, D:F.84, D:F.84, D:F.84, D:F.84 Hydrogen bonds: A:T.408 Water bridges: A:R.480, K:F.4 Salt bridges: K:H.5 PGV.30: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158, P.200 Chain C: H.7, V.9, G.18, A.22, M.25, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84 Ligands: PEK.28, PGV.31 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, A:F.148, A:L.152, A:I.158, A:P.200 Hydrogen bonds: C:W.55, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.31: 28 residues within 4Å: Chain C: L.45, N.48, M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, L.204, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.30, CDL.33 29 PLIP interactions: 27 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:L.45, C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:I.60, C:F.84, C:F.84, C:L.204, C:I.208, C:T.211, C:F.212, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232 Water bridges: C:S.63, C:R.219, C:H.229, C:H.229, F:Q.11, F:E.16 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.32: 12 residues within 4Å: Chain A: F.237 Chain C: T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: N.18 Chain P: W.256 Chain R: S.2 Ligands: CHD.26, DMU.95 10 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 4 interactions with chain H, 1 interactions with chain P Hydrophobic interactions: C:T.93, C:W.97, C:W.97, C:W.97, A:F.237, P:W.256 Water bridges: H:N.16, H:N.18, H:N.18, H:R.21 PGV.64: 32 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, V.155, P.200 Chain P: H.7, V.9, G.18, S.21, A.22, M.25, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, E.88, F.91 Ligands: PEK.84 19 PLIP interactions: 10 interactions with chain P, 9 interactions with chain N Hydrophobic interactions: P:A.22, P:T.26, P:T.51, P:W.55, P:W.55, P:W.55, P:W.56, P:F.91, N:F.148, N:L.152, N:V.155, N:P.200 Hydrogen bonds: P:W.55, N:R.96, N:R.96, N:M.97 Water bridges: P:M.81, N:A.93 Salt bridges: N:R.96 PGV.86: 24 residues within 4Å: Chain P: M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, E.88, L.204, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 27 PLIP interactions: 25 interactions with chain P, 2 interactions with chain Q Hydrophobic interactions: P:W.56, P:W.56, P:W.56, P:W.56, P:W.56, P:I.60, P:F.84, P:F.84, P:L.204, P:I.208, P:T.211, P:F.212, P:F.212, P:F.212 Hydrogen bonds: P:S.63, P:R.219, P:F.231, P:G.232 Water bridges: P:S.63, P:R.219, P:H.229, P:H.229, Q:Q.11, Q:E.16 Salt bridges: P:R.219, P:R.219, P:H.229 PGV.87: 10 residues within 4Å: Chain N: F.237, W.288 Chain P: T.93, W.97, Y.100, H.101, L.104, A.105 Ligands: CDL.46, CHD.81 6 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 3 interactions with chain P Hydrophobic interactions: N:F.237, N:W.288, P:T.93, P:W.97, P:W.97 Water bridges: O:R.178

46 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 2 residues within 4Å: Chain A: P.131, D.221 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.43 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.29, N.31, P.49, R.55 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103, W.104 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligands: CHD.20 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: K.265, T.489 Chain F: I.69 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain A: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502 Chain L: N.9 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.35 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain A: L.433, S.434, G.435 Chain B: F.9, Q.10, M.17, P.166, S.167 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: M.1, Q.10, D.11, S.167 Chain D: V.125, A.126 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.21 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain D: K.118, L.121, D.122, W.135 Chain K: P.45 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain E: Y.13, K.16, E.23 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: K.53 Chain E: L.88, N.89, G.92, I.93, S.94 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.66, T.67, V.68, W.70 Ligands: EDO.10 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain A: Y.510 Chain F: P.35, K.36, T.38, N.46, L.47 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain C: H.229 Chain F: D.8, E.16 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain C: G.118 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain C: F.33 Chain G: K.58, P.59, S.61 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain N: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.98 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain N: Y.260, Y.261, V.394, H.395, P.398, W.494 Ligand excluded by PLIP EDO.67: 7 residues within 4Å: Chain N: E.507 Chain P: T.3 Chain Q: P.29, N.31, P.49, R.55 Ligands: EDO.102 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain N: L.136, A.137 Chain O: Q.103, W.104 Ligands: EDO.69 Ligand excluded by PLIP EDO.69: 6 residues within 4Å: Chain N: Q.52, A.120, A.137, H.138, A.139 Ligands: EDO.68 Ligand excluded by PLIP EDO.70: 2 residues within 4Å: Chain N: P.131, D.221 Ligand excluded by PLIP EDO.71: 7 residues within 4Å: Chain N: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain N: K.265, T.489 Chain Q: I.69, P.82, S.83 Ligand excluded by PLIP EDO.77: 7 residues within 4Å: Chain N: Y.447 Chain O: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.78: 3 residues within 4Å: Chain O: T.125, L.135, F.206 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain O: Q.103, W.104, Y.105, Y.121, N.203 Ligand excluded by PLIP EDO.80: 2 residues within 4Å: Chain O: E.157 Ligands: EDO.93 Ligand excluded by PLIP EDO.93: 5 residues within 4Å: Chain N: P.222, A.223 Chain O: G.177 Chain P: E.109 Ligands: EDO.80 Ligand excluded by PLIP EDO.94: 2 residues within 4Å: Chain P: Q.2, H.68 Ligand excluded by PLIP EDO.98: 7 residues within 4Å: Chain N: T.489, T.490 Chain Q: S.66, T.67, V.68, W.70 Ligands: EDO.65 Ligand excluded by PLIP EDO.99: 6 residues within 4Å: Chain N: Y.510 Chain Q: P.35, K.36, T.38, N.46, L.47 Ligand excluded by PLIP EDO.100: 4 residues within 4Å: Chain Q: F.71, Q.79, R.80, P.82 Ligand excluded by PLIP EDO.101: 4 residues within 4Å: Chain P: P.71, H.229 Chain Q: D.8, E.16 Ligand excluded by PLIP EDO.102: 6 residues within 4Å: Chain N: Y.510 Chain Q: N.31, P.35, P.49, R.55 Ligands: EDO.67 Ligand excluded by PLIP EDO.103: 5 residues within 4Å: Chain Q: A.23, Q.27, D.28, I.32, L.33 Ligand excluded by PLIP EDO.104: 1 residues within 4Å: Chain Q: H.93 Ligand excluded by PLIP EDO.107: 6 residues within 4Å: Chain P: G.118 Chain R: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.108: 4 residues within 4Å: Chain R: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP

2 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.19: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204 CUA.75: 6 residues within 4Å: Chain O: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain O Metal complexes: O:H.161, O:C.196, O:C.196, O:E.198, O:C.200, O:C.200, O:H.204

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.20: 14 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain R: R.14, R.17, F.18, F.21, G.22 Ligands: EDO.15, PEK.85 13 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 7 interactions with chain R Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, R:F.21 Hydrogen bonds: B:Q.59, B:E.62 Water bridges: R:R.14, R:R.17, R:R.17, R:R.17 Salt bridges: R:R.14, R:R.17 CHD.26: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Chain P: L.125 Ligands: PGV.32, CDL.106 10 PLIP interactions: 5 interactions with chain A, 2 interactions with chain P, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, P:L.125, C:W.97 Hydrogen bonds: A:T.301, C:W.97 Water bridges: A:T.301, P:W.256 Salt bridges: A:H.233, C:H.101 CHD.34: 5 residues within 4Å: Chain C: R.154, F.162, F.217, L.221 Chain J: F.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:F.162, C:F.162, C:F.162, C:F.217, C:L.221, J:F.1 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.47: 12 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: E.62, T.63, T.66 Ligands: PEK.29 15 PLIP interactions: 4 interactions with chain O, 7 interactions with chain G, 4 interactions with chain N Hydrophobic interactions: O:T.66, G:F.21, N:M.271, N:W.275, N:W.275, N:W.275 Hydrogen bonds: O:E.62, O:T.63 Water bridges: O:T.63, G:R.17, G:R.17, G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.52: 6 residues within 4Å: Chain A: I.3 Chain J: Y.32, R.33, M.36, T.37, L.40 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:Y.32, J:R.33, J:T.37, J:L.40, A:I.3 Water bridges: J:R.33 CHD.81: 9 residues within 4Å: Chain C: L.125 Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.97, H.101 Ligands: PGV.87 11 PLIP interactions: 1 interactions with chain C, 7 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: C:L.125, N:W.288, N:Y.304, P:W.97 Hydrogen bonds: N:T.301, P:W.97 Water bridges: N:D.298, N:D.300, N:T.301 Salt bridges: N:H.233, P:H.101 CHD.89: 6 residues within 4Å: Chain P: R.154, Q.159, F.162, F.217, L.221 Chain S: F.1 9 PLIP interactions: 7 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:F.162, P:F.162, P:F.162, P:F.217, P:L.221, S:F.1 Water bridges: P:Q.159 Salt bridges: P:R.154 Hydrogen bonds: S:F.1 CHD.109: 7 residues within 4Å: Chain N: L.7, F.8 Chain S: Y.32, R.33, M.36, T.37, L.40 7 PLIP interactions: 7 interactions with chain S Hydrophobic interactions: S:Y.32, S:R.33, S:M.36, S:T.37 Hydrogen bonds: S:Y.32, S:Y.32, S:R.33

6 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.28: 20 residues within 4Å: Chain A: H.151, L.210, L.215 Chain C: W.32, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.30 15 PLIP interactions: 8 interactions with chain G, 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: G:W.62, G:F.69, C:W.32, C:I.186, C:F.201, C:F.201, A:L.210, A:L.215 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.186 Water bridges: G:F.69, G:F.69 PEK.29: 11 residues within 4Å: Chain C: Q.159, I.163, T.166, L.167, Y.170 Chain G: F.21, P.26, W.36 Chain N: W.275, S.279 Ligands: CHD.47 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain N Hydrophobic interactions: C:L.167, C:Y.170, C:Y.170, C:Y.170, N:W.275 Hydrogen bonds: C:Q.159 PEK.83: 8 residues within 4Å: Chain P: I.82, V.89, T.93, F.96, W.238, V.245, V.246, F.249 8 PLIP interactions: 8 interactions with chain P Hydrophobic interactions: P:I.82, P:V.89, P:F.96, P:F.96, P:W.238, P:W.238, P:V.245, P:V.246 PEK.84: 28 residues within 4Å: Chain N: H.151, V.155, A.203, L.210, L.215 Chain P: W.32, F.33, T.172, Q.175, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, G.203, I.207 Chain R: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.64 21 PLIP interactions: 9 interactions with chain P, 4 interactions with chain N, 8 interactions with chain R Hydrophobic interactions: P:W.32, P:F.33, P:Q.175, P:I.186, P:F.201, P:F.201, P:F.201, P:I.207, N:V.155, N:A.203, N:L.210, N:L.215, R:W.62, R:F.69 Hydrogen bonds: P:I.186, R:T.68, R:F.70, R:N.76, R:N.76 Water bridges: R:F.69, R:F.69 PEK.85: 13 residues within 4Å: Chain A: W.275, S.279, I.311 Chain B: T.66 Chain P: I.163, T.166, L.167, Y.170 Chain R: R.17, F.21, L.25 Ligands: CHD.20, CDL.106 9 PLIP interactions: 2 interactions with chain A, 2 interactions with chain R, 5 interactions with chain P Hydrophobic interactions: A:W.275, A:I.311, R:F.21, R:L.25, P:T.166, P:L.167, P:Y.170, P:Y.170, P:Y.170 PEK.105: 10 residues within 4Å: Chain C: I.82, L.83, V.89, T.93, F.96, W.238, V.245, F.249 Chain R: G.6 Ligands: CDL.106 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.82, C:I.82, C:L.83, C:V.89, C:F.96, C:F.96, C:W.238, C:V.245, C:V.245, C:F.249

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.33: 27 residues within 4Å: Chain C: T.46, M.49, L.50, M.52, Y.53, W.56, R.57, I.60, R.61, F.65, G.168, V.169, T.172, I.207, S.210, T.211, I.214, V.215, F.218, R.219, K.222, H.224 Chain J: K.8, F.12, L.31, V.34 Ligands: PGV.31 30 PLIP interactions: 23 interactions with chain C, 7 interactions with chain J Hydrophobic interactions: C:M.49, C:L.50, C:Y.53, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:I.60, C:V.169, C:T.172, C:I.207, C:T.211, C:F.218, J:L.31, J:V.34 Hydrogen bonds: C:Y.53 Water bridges: C:R.57, C:R.61, J:K.8, J:G.24, J:T.27 Salt bridges: C:R.61, C:K.222, C:K.222, C:K.222, C:H.224, J:K.8, J:K.8 CDL.46: 27 residues within 4Å: Chain C: N.123, L.125, L.129, V.140, V.252 Chain G: L.19, L.23, S.27, L.30, N.34, L.37, H.38 Chain N: F.282, I.286, D.300, Y.304, S.307, A.308, I.311 Chain O: A.70, L.73, I.74, A.77, L.78, L.81, Y.85 Ligands: PGV.87 19 PLIP interactions: 3 interactions with chain C, 6 interactions with chain N, 4 interactions with chain O, 6 interactions with chain G Hydrophobic interactions: C:V.140, C:V.252, N:F.282, N:I.286, N:Y.304, N:A.308, N:I.311, O:L.73, O:A.77, O:L.78, O:L.81, G:L.19, G:L.23, G:L.30 Hydrogen bonds: C:N.123, G:N.34, G:H.38 Water bridges: N:D.300 Salt bridges: G:H.38 CDL.88: 19 residues within 4Å: Chain P: T.46, M.49, L.50, Y.53, W.56, R.57, I.60, R.61, V.169, T.172, I.207, S.210, T.211, I.214, V.215, F.218, K.222 Chain S: F.12, L.31 19 PLIP interactions: 17 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:T.46, P:M.49, P:Y.53, P:Y.53, P:W.56, P:W.56, P:R.57, P:I.60, P:V.169, P:T.172, P:I.207, P:I.214, P:V.215, P:F.218, S:L.31, S:L.31 Hydrogen bonds: P:Y.53 Water bridges: P:R.57 Salt bridges: P:R.61 CDL.106: 32 residues within 4Å: Chain A: F.282, I.286, D.300, A.303, Y.304, S.307, A.308, I.311, I.314 Chain B: A.70, L.73, I.74, A.77, L.78, L.81, R.82, Y.85 Chain P: N.123, L.125, L.129, L.136, V.140 Chain R: L.23, S.27, L.30, L.33, N.34, L.37, H.38 Ligands: CHD.26, PEK.85, PEK.105 24 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B, 7 interactions with chain R, 2 interactions with chain P Hydrophobic interactions: A:F.282, A:F.282, A:I.286, A:A.303, A:Y.304, A:A.308, A:I.311, A:I.314, B:A.70, B:L.73, B:I.74, B:L.78, B:L.81, B:L.81, R:L.23, R:L.30, R:L.30, R:N.34, R:L.37, P:L.136 Hydrogen bonds: B:Y.85, R:N.34, P:N.123 Salt bridges: R:H.38

13 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.36: 9 residues within 4Å: Chain C: N.36, S.37, T.39, I.43 Chain J: L.38, G.41, G.42, Y.45 Ligands: DMU.51 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain J Hydrophobic interactions: C:I.43, J:L.38, J:Y.45, J:Y.45, J:Y.45 Hydrogen bonds: C:N.36, C:N.36, C:S.37, J:Y.45 DMU.50: 5 residues within 4Å: Chain C: W.32, M.38 Chain G: W.62, G.63, F.69 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:W.32, C:W.32, C:W.32 Hydrogen bonds: G:G.63, G:F.69 DMU.51: 13 residues within 4Å: Chain A: L.145 Chain C: L.23, S.27, T.30, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.36 9 PLIP interactions: 5 interactions with chain C, 3 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: C:L.23, C:T.30, C:M.31, C:F.35, C:F.35, J:L.50, A:L.145 Hydrogen bonds: J:Y.45, J:Y.45 DMU.53: 6 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 Ligands: DMU.54 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:V.21, K:W.24, K:W.24, K:W.24, K:V.25, D:I.86 DMU.54: 6 residues within 4Å: Chain K: W.24, V.25, A.28, T.29 Ligands: DMU.53, DMU.55 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:W.24, K:V.25, K:A.28 DMU.55: 4 residues within 4Å: Chain K: A.28, T.29, W.35 Ligands: DMU.54 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:T.29, K:W.35, K:W.35 DMU.56: 8 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: F.37, I.38, R.40, H.41, L.44, K.45 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:I.38 Hydrogen bonds: L:R.40, L:H.41 Salt bridges: L:H.41 DMU.57: 12 residues within 4Å: Chain A: F.459 Chain D: W.95, Y.99 Chain L: F.36 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 14 PLIP interactions: 6 interactions with chain M, 6 interactions with chain D, 1 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: M:L.27, M:A.30, M:L.34, D:W.95, D:W.95, D:W.95, L:F.36, A:F.459 Water bridges: M:W.32, M:H.36, M:H.36, D:Y.99, D:Y.99, D:Y.99 DMU.90: 12 residues within 4Å: Chain P: M.31, N.36, S.37, T.39, I.43 Chain S: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.91, DMU.92 11 PLIP interactions: 6 interactions with chain P, 5 interactions with chain S Hydrophobic interactions: P:T.39, S:L.38, S:Y.45, S:Y.45, S:Y.45 Hydrogen bonds: P:N.36, P:N.36, P:S.37, P:S.37, P:S.37, S:Y.45 DMU.91: 6 residues within 4Å: Chain P: N.36, S.37, M.38, T.39 Ligands: DMU.90, DMU.96 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain R Hydrophobic interactions: P:T.39 Hydrogen bonds: P:N.36, P:S.37, P:M.38, P:T.39, R:S.61 DMU.92: 12 residues within 4Å: Chain N: L.110, A.114, L.145 Chain P: S.27, M.31, F.35 Chain S: Y.45, S.46, Y.48, C.49, W.52 Ligands: DMU.90 8 PLIP interactions: 3 interactions with chain N, 2 interactions with chain S, 3 interactions with chain P Hydrophobic interactions: N:L.110, N:A.114, N:L.145, P:M.31, P:F.35, P:F.35 Hydrogen bonds: S:Y.45, S:Y.45 DMU.95: 7 residues within 4Å: Chain P: W.114, P.115, V.252, W.256, W.257, S.259 Ligands: PGV.32 8 PLIP interactions: 8 interactions with chain P Hydrophobic interactions: P:V.252, P:W.256, P:W.256 Hydrogen bonds: P:W.114, P:W.257 Water bridges: P:W.114, P:S.259, P:S.259 DMU.96: 7 residues within 4Å: Chain P: L.29, W.32, M.38 Chain R: W.62, G.63, F.69 Ligands: DMU.91 5 PLIP interactions: 2 interactions with chain R, 3 interactions with chain P Hydrophobic interactions: R:F.69, P:L.29, P:W.32, P:W.32 Hydrogen bonds: R:G.63

2 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.39: 22 residues within 4Å: Chain A: F.321, L.324, H.328 Chain B: I.41, H.52, M.56, D.57, E.60, V.61, I.64, W.65, L.68, P.69, I.72 Chain E: E.1, D.3, F.6, D.35, L.36 Chain I: R.10, A.14, L.17 15 PLIP interactions: 7 interactions with chain B, 3 interactions with chain I, 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: B:I.41, B:V.61, B:W.65, B:L.68, B:L.68, B:P.69, B:I.72, I:A.14, I:L.17, A:F.321, A:F.321, A:L.324 Water bridges: I:A.14 Hydrogen bonds: E:D.35 Salt bridges: E:D.3 PSC.76: 13 residues within 4Å: Chain N: F.268, F.321, A.325, H.328 Chain O: I.41, H.52, M.56, D.57, E.60, V.61, W.65, L.68, P.69 14 PLIP interactions: 10 interactions with chain O, 4 interactions with chain N Hydrophobic interactions: O:I.41, O:M.56, O:V.61, O:W.65, O:L.68, O:L.68, O:P.69, N:F.268, N:F.321, N:F.321, N:A.325 Hydrogen bonds: O:D.57 Water bridges: O:H.52 Salt bridges: O:H.52

2 x ZN: ZINC ION(Non-covalent)

ZN.42: 4 residues within 4Å: Chain F: C.59, C.61, C.81, C.84 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.59, F:C.61, F:C.81, F:C.84 ZN.97: 4 residues within 4Å: Chain Q: C.59, C.61, C.81, C.84 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.59, Q:C.61, Q:C.81, Q:C.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J.Biol.Chem. (2023)

Release Date

2022-12-07

Peptides

Cytochrome c oxidase subunit 1: AN
Cytochrome c oxidase subunit 2: BO
Cytochrome c oxidase subunit 3: CP
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: FQ
Cytochrome c oxidase subunit 6A2, mitochondrial: GR
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1, mitochondrial: JS
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B, mitochondrial: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
N

B
B

O
O

C
C

P
P

D
D

E
E

F
F

Q
S

G
G

R
T

H
H

I
I

J
J

S
W

K
K

L
L

M
M

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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